| 141. |
- Olson, Nathan D., et al.
(författare)
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precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 142. |
- Olson, Nathan D., et al.
(författare)
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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
- 2022
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 143. |
- Olsson, Erik J, et al.
(författare)
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Hilpinen's Theory of Inquiry
- 2022
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Ingår i: Agency, Norms, Inquiry, and Artifacts : Essays in Honor of Risto Hilpinen - Essays in Honor of Risto Hilpinen. - Cham : Springer International Publishing. - 2542-8292 .- 0166-6991. - 9783030907495 - 9783030907518 - 9783030907488 ; 454, s. 175-191
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Bokkapitel (refereegranskat)abstract
- Risto Hilpinen’s name is associated with seminal contributions to many areas of analytic philosophy, including influential work on deontic logic and the theory of artifacts, as well as important early investigations into inductive logic and indefeasibility analyses of knowledge. A somewhat lesser known body of Hilpinen’s work concerns the theory of inquiry, whereby the central questions are how to conceptualize and understand human investigations from a general epistemological perspective. The present contribution traces the development of Hilpinen’s theory of inquiry through his main contributions to the topic in the 1980s and 1990s with special attention to how the problems in the initial formulation of the theory were eventually given more detailed and convincing solutions.
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| 144. |
- Pignolo, Robert J., et al.
(författare)
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Reduction of new heterotopic ossification (HO) in the open-label, phase 3 MOVE trial of palovarotene for fibrodysplasia ossificans progressiva (FOP)
- 2023
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Ingår i: Journal of Bone and Mineral Research. - : John Wiley & Sons. - 0884-0431 .- 1523-4681. ; 38:3, s. 381-394
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Tidskriftsartikel (refereegranskat)abstract
- Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare, severely disabling genetic disorder of progressive heterotopic ossification (HO). The single-arm, open-label, phase 3 MOVE trial (NCT03312634) assessed efficacy and safety of palovarotene, a selective retinoic acid receptor gamma agonist, in patients with FOP. Findings were compared with FOP natural history study (NHS; NCT02322255) participants untreated beyond standard of care. Patients aged ≥4 years received palovarotene once daily (chronic: 5 mg; flare-up: 20 mg for 4 weeks, then 10 mg for ≥8 weeks; weight-adjusted if skeletally immature). The primary endpoint was annualized change in new HO volume versus NHS participants (by low-dose whole-body computed tomography [WBCT]), analyzed using a Bayesian compound Poisson model (BcPM) with square-root transformation. Twelve-month interim analyses met futility criteria; dosing was paused. An independent Data Monitoring Committee recommended trial continuation. Post hoc 18-month interim analyses utilized BcPM with square-root transformation and HO data collapsed to equalize MOVE and NHS visit schedules, BcPM without transformation, and weighted linear mixed-effects (wLME) models, alongside prespecified analysis. Safety was assessed throughout. Eighteen-month interim analyses included 97 MOVE and 101 NHS individuals with post-baseline WBCT. BcPM analyses without transformation showed 99.4% probability of any reduction in new HO with palovarotene versus NHS participants (with transformation: 65.4%). Mean annualized new HO volume was 60% lower in MOVE versus the NHS. wLME results were similar (54% reduction fitted; nominal p = 0.039). All palovarotene-treated patients reported ≥1 adverse event (AE); 97.0% reported ≥1 retinoid-associated AE; 29.3% reported ≥1 serious AE, including premature physeal closure (PPC)/epiphyseal disorder in 21/57 (36.8%) patients aged <14 years. Post hoc computational analyses using WBCT showed decreased vertebral bone mineral density, content, and strength, and increased vertebral fracture risk in palovarotene-treated patients. Thus, post hoc analyses showed evidence for efficacy of palovarotene in reducing new HO in FOP, but high risk of PPC in skeletally immature patients.
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| 145. |
- Pignolo, Robert J., et al.
(författare)
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The effects of palovarotene in patients with fibrodysplasia ossificans progressiva : a plain language summary
- 2023
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Ingår i: Future Rare Diseases. - : Future Medicine. - 2399-5270 .- 2399-5262. ; 3:1
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Forskningsöversikt (refereegranskat)abstract
- What is this summary about?This is a plain language summary of an article originally published in the Journal of Bone and Mineral Research. People with fibrodysplasia ossificans progressiva (FOP) become physically disabled over time as new bone forms in places where it is not usually found, such as in muscles and ligaments. Until recently, there were no treatments for FOP that had been proven through clinical trials; however, a drug called palovarotene has been tested in clinical trials and may be effective. Here, we describe the MOVE trial, which investigated how effectively palovarotene works, as well as its safety in treating patients with FOP.What were the results?Results from MOVE suggest that palovarotene may reduce extra bone formation outside the normal skeleton. Patients with FOP who took palovarotene formed less new bone than those who did not take palovarotene. The most common side effects involved the skin, and included dryness and irritation. Some children who were still growing when they took palovarotene had a side effect that resulted in the (normal) growth of their skeleton stopping too soon.What do the results of the trial mean?Palovarotene may be a useful treatment option for FOP. Patients, caregivers, and doctors would need to consider the benefits and risks of treatment with palovarotene, particularly with growing children.
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| 146. |
- Porter, Richard T. J., et al.
(författare)
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Techno-economic assessment of CO2 quality effect on its storage and transport : CO(2)QUEST An overview of aims, objectives and main findings
- 2016
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Ingår i: International Journal of Greenhouse Gas Control. - : Elsevier BV. - 1750-5836 .- 1878-0148. ; 54, s. 662-681
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Tidskriftsartikel (refereegranskat)abstract
- This paper provides an overview of the aims, objectives and the main findings of the CO(2)QUEST FP7 collaborative project, funded by the European Commission and designed to address the fundamentally important and urgent issues regarding the impact of the typical impurities in CO2 streams captured from fossil fuel power plants and other CO2 intensive industries on their safe and economic pipeline transportation and storage. The main features and results recorded from some of the unique test facilities constructed as part of the project are presented. These include an extensively instrumented realistic-scale test pipeline for conducting pipeline rupture and dispersion tests in China, an injection test facility in France to study the mobility of trace metallic elements contained in a CO2 stream following injection near a shallow-water qualifier and fluid/rock interactions and well integrity experiments conducted using a fully instrumented deep-well CO2/impurities injection test facility in Israel. The above, along with the various unique mathematical models developed, provide the fundamentally important tools needed to define impurity tolerance levels, mixing protocols and control measures for pipeline networks and storage infrastructure, thus contributing to the development of relevant standards for the safe design and economic operation of CCS.
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| 147. |
- Rasmus, Sirpa, et al.
(författare)
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Recent Change - Terrestrial Cryosphere
- 2015
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Ingår i: Second Assessment of Climate Change for the Baltic Sea Basin. - Cham : Springer. - 9783319160054 - 9783319160061 ; , s. 117-129
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Bokkapitel (refereegranskat)abstract
- This chapter compiles and assesses information on recent and current change within the terrestrial cryosphere of the Baltic Sea drainage basin. Findings are based on long-term observations. Snow cover extent (SCE), duration and amount have shown a widespread decrease although there is large interannual and regional variation. Few data are available on changes in snow structural properties. There is no evidence for a recent change in the frequency or severity of snow-related extreme events. There has been a decrease in glacier coverage in Sweden and glacier ice thickness in inland Scandinavia. The European permafrost is warming, and there has been a northward retreat of the southern boundary of near-surface permafrost in European Russia.
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| 148. |
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| 149. |
- Rosenthal, Mark A, et al.
(författare)
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Phase I and Pharmacokinetic Evaluation of Intravenous Hyaluronic Acid in Combination with Doxorubicin or 5-Fluorouracil
- 2005
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Ingår i: Chemotherapy. - : S. Karger AG. - 0009-3157 .- 1421-9794. ; 51:2-3, s. 132-141
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Pre-clinically, hyaluronan (HA) has been demonstrated to systemically target chemotherapeutic drugs to tumours while ameliorating treatment toxicities. This study is a preliminary clinical investigation to determine if HA could be safely used in combination with 5-fluorouracil (5-FU) and doxorubicin (DOX). METHODS: Thirty patients with metastatic cancer were intravenously administered 500 mg/m2 HA in combination with escalating doses of DOX (30-60 mg/m2) or 5-FU (cumulative dose of 1,350-2,250 mg/m2 per cycle). The effect of pre-administration of 20 mg/m2 of folinic acid on HA/5-FU chemotherapy was also investigated. Patients were randomized to receive either HA/chemotherapy or chemotherapy alone in their first treatment cycle and vice versa for the second cycle. Patients received HA and chemotherapy in all subsequent cycles. RESULTS: Treatment was well tolerated, tumour responses were observed and the co-administration of HA did not alter the pharmacokinetics of clinically relevant doses of 5-FU or DOX. CONCLUSION: High doses of intravenous high-molecular-weight HA can be safely co-administered with clinical doses of chemotherapy without significantly altering the toxicity or pharmacokinetics of the drugs or HA.
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| 150. |
- Saba, Luca, et al.
(författare)
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Carotid plaque-RADS : a novel stroke risk classification system
- 2024
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Ingår i: JACC Cardiovascular Imaging. - : Elsevier. - 1936-878X .- 1876-7591. ; 17:1, s. 62-75
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Tidskriftsartikel (refereegranskat)abstract
- Background: Carotid artery atherosclerosis is highly prevalent in the general population and is a well-established risk factor for acute ischemic stroke. Although the morphological characteristics of vulnerable plaques are well recognized, there is a lack of consensus in reporting and interpreting carotid plaque features.Objectives: The aim of this document is to establish a consistent and comprehensive approach for imaging and reporting carotid plaque by introducing the Plaque–Reporting and Data System (RADS) score.Methods: A panel of experts recognized the necessity to develop a classification system for carotid plaque and its defining characteristics. Using a multimodality analysis approach, the Plaque-RADS categories were established through consensus, drawing on existing published reports.Results: The authors present a universal classification that is applicable to both researchers and clinicians. The Plaque-RADS score offers a morphological assessment in addition to the prevailing quantitative parameter of “stenosis.” The Plaque-RADS score spans from grade 1 (indicating complete absence of plaque) to grade 4 (representing complicated plaque). Accompanying visual examples are included to facilitate a clear understanding of the Plaque-RADS categories.Conclusions: Plaque-RADS is a standardized and reliable system of reporting carotid plaque composition and morphology via different imaging modalities, such as ultrasound, computed tomography, and magnetic resonance imaging. This scoring system has the potential to help in the precise identification of patients who may benefit from exclusive medical intervention and those who require alternative treatments, thereby enhancing patient care. A standardized lexicon and structured reporting promise to enhance communication between radiologists, referring clinicians, and scientists.
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